Difference between revisions of "Bklein7 Week 4"

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(Created the week 4 individual journal entry)
 
(Added Headings and Outlines)
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==Transcription and Translation "Taken to the Next Level"
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==Transcription and Translation "Taken to the Next Level"==
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# Modify the gene sequence string so that it highlights or “tags” the special sequences within this gene, as follows (ellipses indicate bases in the sequence; note the spaces before the start tag and after the end tag):
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#* -35 box of the promoter <pre>... <minus35box>...</minus35box> ...</pre>
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#* -10 box of the promoter <pre>... <minus10box>...</minus10box> ...</pre>
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#* transcription start site <pre>... <tss>...</tss> ...</pre>
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#* ribosome binding site <pre>... <rbs>...</rbs> ...</pre>
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#* start codon <pre>... <start_codon>...</start_codon> ...</pre>
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#* stop codon <pre>... <stop_codon>...</stop_codon> ...</pre>
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#* terminator <pre>... <terminator>...</terminator> ...</pre>
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# What is the ''exact'' mRNA sequence that is transcribed from this gene?
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# What is the amino acid sequence that is translated from this mRNA?
  
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To do
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==Preliminary Code==
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  sed "s/tt[gt]ac[at]/<minus35box>&<\/minux35box>\n/1" infA-E.coli-K12.txt | sed -r "2s/^.   
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  {17}/&<minus10box>/g" | sed "s/<minus10box>....../&<\/minus10box/g" | sed -r
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  "s/<\/minus10box>.{11}/&<tss>/g" | sed "s/<tss>./&<\/tss/g" | sed "s/gagg/<rbs>&<\/rbs>\n/g"
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  | sed "3s/atg/<start_codon>&<\/start_codon>\n/1" | sed "s/aaaaggt/\n<terminator>&/g" | sed -
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  r "s/aaaaggt.*gcctttt.{4}/&<\/terminator>/g" | sed "4s/.../& /g" | sed -r
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  "4s/taa|tag|tga/<stop_codon>&<\/stop_codon>/g" | sed "4s/ //g" | sed ':a;N;$!ba;s/\n//g'
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*String together redundant sed commands with ; or find a way to make them more compact
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*Verify when the terminator sequence starts
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*Is there a way to count backwards in a line with sed? or so replace only the last instance that matches? previous experiments
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**sed "s/x.*$/y/g" - does not work, wild card overtakes the last instance
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**sed "s/x/y/1$" - does not work
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**answer: use rev commands!
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==Links==
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{{Template:Bklein7}}
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[[Category:Journal Entry]]

Revision as of 18:51, 28 September 2015

Transcription and Translation "Taken to the Next Level"

  1. Modify the gene sequence string so that it highlights or “tags” the special sequences within this gene, as follows (ellipses indicate bases in the sequence; note the spaces before the start tag and after the end tag):
    • -35 box of the promoter 
      ... <minus35box>...</minus35box> ...
    • -10 box of the promoter 
      ... <minus10box>...</minus10box> ...
    • transcription start site 
      ... <tss>...</tss> ...
    • ribosome binding site 
      ... <rbs>...</rbs> ...
    • start codon 
      ... <start_codon>...</start_codon> ...
    • stop codon 
      ... <stop_codon>...</stop_codon> ...
    • terminator 
      ... <terminator>...</terminator> ...
  2. What is the exact mRNA sequence that is transcribed from this gene?
  3. What is the amino acid sequence that is translated from this mRNA?

Preliminary Code

 sed "s/tt[gt]ac[at]/<minus35box>&<\/minux35box>\n/1" infA-E.coli-K12.txt | sed -r "2s/^.    
 {17}/&<minus10box>/g" | sed "s/<minus10box>....../&<\/minus10box/g" | sed -r 
 "s/<\/minus10box>.{11}/&<tss>/g" | sed "s/<tss>./&<\/tss/g" | sed "s/gagg/<rbs>&<\/rbs>\n/g" 
 | sed "3s/atg/<start_codon>&<\/start_codon>\n/1" | sed "s/aaaaggt/\n<terminator>&/g" | sed -
 r "s/aaaaggt.*gcctttt.{4}/&<\/terminator>/g" | sed "4s/.../& /g" | sed -r 
 "4s/taa|tag|tga/<stop_codon>&<\/stop_codon>/g" | sed "4s/ //g" | sed ':a;N;$!ba;s/\n//g'
  • String together redundant sed commands with ; or find a way to make them more compact
  • Verify when the terminator sequence starts
  • Is there a way to count backwards in a line with sed? or so replace only the last instance that matches? previous experiments
    • sed "s/x.*$/y/g" - does not work, wild card overtakes the last instance
    • sed "s/x/y/1$" - does not work
    • answer: use rev commands!

Links

Assignments Pages

Individual Journal Entries

Shared Journal Entries

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